Project 1157: Sergei Tarasov, François Génier. 2015. Innovative Bayesian and Parsimony Phylogeny of Dung Beetles (Coleoptera, Scarabaeidae, Scarabaeinae) Enhanced by Ontology-Based Partitioning of Morphological Characters. PLOS ONE. 10 (3):1-86.

Abstract

Scarabaeine dung beetles are the dominant dung feeding group of insects and are widely used as model organisms in conservation, ecology and developmental biology. Due to the conflicts among 13 recently published phylogenies dealing with the higher-level relationships of dung beetles, the phylogeny of this lineage remains largely unresolved. In this study, we conduct rigorous phylogenetic analyses of dung beetles, based on an unprecedented taxon sample (110 taxa) and detailed investigation of morphology (205 characters). We provide the description of morphology and thoroughly illustrate the used characters. Along with parsimony, traditionally used in the analysis of morphological data, we also apply the Bayesian method with a novel approach that uses anatomy ontology for matrix partitioning. This approach allows for heterogeneity in evolutionary rates among characters from different anatomical regions. Anatomy ontology generates a number of parameter-partition schemes which we compare using Bayes factor. We also test the effect of inclusion of autapomorphies in the morphological analysis, which hitherto has not been examined. Generally, schemes with more parameters were favored in the Bayesian comparison suggesting that characters located on different body regions evolve at different rates and that partitioning of the data matrix using anatomy ontology is reasonable; however, trees from the parsimony and all the Bayesian analyses were quite consistent. The hypothesized phylogeny reveals many novel clades and provides additional support for some clades recovered in previous analyses. Our results provide a solid basis for a new classification of dung beetles, in which the taxonomic limits of the tribes Dichotomiini, Deltochilini and Coprini are restricted and many new tribes must be described. Based on the consistency of the phylogeny with biogeography, we speculate that dung beetles may have originated in the Mesozoic contrary to the traditional view pointing to a Cenozoic origin.


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Article DOI: 10.1371/journal.pone.0116671

Project DOI: 10.7934/P1157, http://dx.doi.org/10.7934/P1157
This project containsMatrices
  • 20 Media
  • 1 Matrix
  • 110 Taxa
  • 19 Specimens
  • 205 Characters
Total size of project's media files: 16 MB

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Total scored cells: 22528
Total media associated with cells: 0
Total labels associated with cell media: 0
Characters
Total characters: 205
Total characters with associated media: 0
Total characters with media with labels: 0
Total character states: 412
Total character states with associated media: 0
Total character states with media with labels:0
Total unordered/ordered characters:205/0
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MorphoBank Project 1157


    Members

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    Sergei Tarasov
    Project Administrator
    Last logged in 03/18/15
    110192019205000022528
    (21940, 0, 588)
    07000
    François Génier
    Full membership
    Last logged in Never
    0000000000
    (0, 0, 0)
    00000


    Taxonomic Overview for Matrix 'M2579' (110 Taxa)

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    [1] Aphodius erraticus
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    [2] Podotenus fulviventris
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    [3] Aulonocnemis crassecostata
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    [4] Manjarivolo sp
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    [5] Coptorhina auspicata
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    [6] Delopleurus sp
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    [7] Frankenbergerius armatus
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    [8] Sarophorus costatus
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    [9] Odontoloma sp
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    [10] Nebulasilvius insularis
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    [11] Endroedyolus paradoxus
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    [12] Dicranocara deschodti
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    [13] Byrrhidium namaquensis
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    [14] Paraphytus sp
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    [15] Epirinus sp
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    [16] Neosisyphus sp
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    [17] Macroderes mutilans
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    [18] Xinidium dentilabris
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    [19] Pedaria sp
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    [20] Gyronotus carinatus
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    [21] Anachalcos convexus
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    [22] Hammondantus psammophilus
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    [23] Pycnopanelus krikkeni
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    [24] Janssensantus pauliani
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    [25] Aphengoecus multiserratus
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    [26] Bohepilissus sp
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    [27] Circellium bacchus
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    [28] Dwesasilvasedis medinae
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    [29] Coptodactyla nitida
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    [30] Amphistomus calcaratus
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    [31] Aulacopris maximus
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    [32] Canthonosoma macleayi
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    [33] Boletoscapter cornutus
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    [34] Gen. nov. sp. nov.
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    [35] Cephalodesmius armiger
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    [36] Coproecus hemisphaericus
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    [37] Demarziella interrupta
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    [38] Diorygopyx tibialis
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    [39] Mentophilus hollandiae
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    [40] Onthobium gutierrez
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    [41] Pseudonthobium sinuatotibiale
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    [42] Tesserodon erratum
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    [43] Saphobius sp
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    [44] Bdelyrus seminudus
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    [45] Tesserodoniella elguetai
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    [46] Canthochilum tureyra
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    [47] Canthonella silphoides
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    [48] Cryptocanthon paradoxus
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    [49] Paracanthon sp sp n
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    [50] Streblopus opatroides
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    [51] Zonocopris gibbicollis
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    [52] Genieridium margareteae
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    [53] Onoreidium howdeni
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    [54] Trichillum pauliani
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    [55] Scatimus strandi
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    [56] Aphengium cupreum
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    [57] Ateuchus squalidus
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    [58] Ateuchus histeroides
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    [59] Agamopus lampros
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    [60] Agamopus viridis
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    [61] Canthidium bokermanni
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    [62] Chalcocopris hesperus
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    [63] Dichotomius sp
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    [64] Dichotomius sericeus
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    [65] Homocopris torulosus
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    [66] Ontherus appendiculatus
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    [67] Uroxys latesulcatus
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    [68] Uroxys epipleuralis
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    [69] Uroxys pauliani
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    [70] Bdelyropsis bowditchi
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    [71] Canthon virens
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    [72] Malagoniella yucateca
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    [73] Megathoposoma candezei
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    [74] Scybalophagus rugosus
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    [75] Deltochilum sp
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    [76] Scybalocanthon nigriceps
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    [77] Hansreia sp
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    [78] Silvicanthon bridarollii
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    [79] Tetraechma sanguineomaculata
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    [80] Anomiopus edmondsi
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    [81] Scatonomus fasciculatus
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    [82] Sinapisoma sp
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    [83] Heliocopris sp
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    [84] Catharsius sp
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    [85] Metacatharsius sp
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    [86] Copris sp
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    [87] Pseudopedaria grossa
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    [88] Microcopris sp
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    [89] Gromphas aeruginosa
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    [90] Coprophanaeus telamon
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    [91] Oruscatus davus
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    [92] Phanaeus splendidulus
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    [93] Ennearabdus lobocephalus
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    [94] Eucranium arachnoides
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    [95] Glyphoderus monticola
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    [96] Eurysternus hamaticollis
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    [97] Pachysoma aesculapius
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    [98] Scarabaeus aegyptiorum
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    [99] Paragymnopleurus sp
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    [100] Gymnopleurus leei
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    [101] Epactoides sp1
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    [102] Epactoides sp2
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    [103] Ochicanthon sp
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    [104] Apotolamprus quadrimaculatus
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    [105] Arachnodes sp
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    [106] Tanzanolus sp
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    [107] Onthophagus avocetta
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    [108] Helictopleurus quadripunctatus
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    [109] Bubas bison
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    [110] Onitis sp
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    Taxon list8880
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